The Official Deleted/Alternate Material Thread

Nothing is unwelcome, all is accepted. Have at it.
I am intending this as a reference thread for people tired of scouring the internet for this information. If something new is found, it goes in the list.
Let me just start you off.

TMP:
The film's NATO trailer showcased a shot of the Klingon commander yelling at camera, later used in the theatrical version's video screen sequence. It's possible this shot was originally filmed in widescreen.
Original special effects for opening, showcasing the actual destruction of the vessels, rather than dissolution
English dialogue for the Vulcan elders during the Kohlinar. Different versions translate the Vulcan dialogue differently, but no subtitled versions match the original English dialogue.
Cut special effects shot of StarFleet HQ.
Kirk defends Deltans when Uhura expresses suprise at Illia's inclusion on the crew list.
An alternate version of McCoy's arrival was shot, showing him carrying a riding crop.
Kirk notifies the crew of the ship preparing for launch via wall communicator.
Early trailers show a shot of the Enterprise's deflector dish igniting, from head on.
The original teaser featured an alternate shot of Kirk saying "Take us out"
A shortened frontal view of the Enterprise was used in TMP, but the complete version appears in a trailer as well as TWOK.
An unidentified shot of Scotty scanning the warp core with some device, possibly part of the activation montage.
The original wormhole effect, a much more crowded and scary looking effect, as appearing in the work print.
The entire wormhole sequence appears without effects and sound editing in the film's NATO trailer.
The original asteroid explosion, different from the stock effect used in the film.
A line was cut from Mr. Spock's arrival from Dr McCoy "Never look a gift Vulcan in the ears, Jim".
The comic version contains a different conversation in the officer's lounge, more dwelling on Spock's decision to become a full Vulcan. This was additional dialogue in the script.
Red alert shots cut out and used in TWOK.
A much longer scene of the first torpedo attack, including Chekov recoiling in pain much longer.
Chapel shares a strange moment with Illia before spraying Chekov down, shown in an early trailer.
A security guard is vaporized by the plasma probe.
Decker and Illia's sex? May have been filmed as it is in the novelization, who knows?
The Memory Wall, which still photographs suggest may have been fully filmed.
A short discussion was cut from the sickbay scene.
Illia's tour of engineering.
A small bit of footage was trimmed from the tear scene.
Kirk cancels the self-destruct order before the spacewalk.
The security guard (Phillips) is mentioned by name in Kirk's final log. You can tell in the final cut that his report has been dubbed in.
There were a few takes of the final shot, including one where Spock made a quite humorous joke, but undermined the tone.

TWOK:
A few seconds of footage were cut from the simulator scene.
An interesting note, the IDW comic version of TWOK has exterior shots showing the Enterprise's destruction during the Kobayashi Maru, contrary to every released version of the film.
A brief snippet of deleted footage from the present scene including the statement of Saavik being half-Romulan. Additionally, Spock asks if Kirk is feeling oppressed by something.
A longer take of the McCoy/glasses scene.
Chekov originally had a different log entry, designating he was duty officer.
Carol and David originally had a longer scene with each other.
Chekov spotting a child in the Botany Bay window, and an infamous scene showing a stuntman in blackface standing in for Terrell.
Terrell finding Khan's baby in the Botany Bay.
Marla McGivers (or Noonien Singh?)is mentioned by name in Khan's speech.
The Ceti Eel scene was originally a little longer and more graphic.
Kyle and Beach attempt a rescue, but Terrel (under the eel's power) convinces them to beam aboard Khan's crew.
Like the first film, Spock and Saavik originally spoke English in their conversation.
A scene detailing Sulu's promotion. (BTW Sulu was originally intended to have control of the Excelsior in THIS film.)
An alternate take of the scene of the scientists arguing.
Carol's narration during the Genesis tape scene was changed to give a different explanation of the Genesis effect (actually it was to provide implication that Spock could return).
An alternate take of the discussion in Kirk's quarters.
Kirk had a line about Chekov during the first Reliant encounter.
Scotty is seen telling the other engineers to stay at their posts.
The original cut of the Enterprise's attack had Khan moving across the bridge shouting at Kirk.
At one point Kirk recalls the "blind as a Tiberian bat" line while orbiting Regula 1.
McCoy reveals he had worked with Terrell.
The scene of David attacking Kirk was reshot at the studio's consent, and all subsequent scenes in the cave as well. The original version featured David leaping out of a cargo container, as shown in the IDW comic adaptation.*
A scene showing McCoy working on Chekov's ear, and denying David passage to the bridge.
Chekov later wakes up and is taken to the bridge, David soon follows.
A scene of Khan's baby in the transporter room next to the detonating Genesis device.*
Khan's final reaction shot before the Reliant' destruction.
The original funeral scene was slightly longer.
The scene between David and Kirk had different dialogue initially, redubbed at the studio's consent. "I should be on the bridge" "Are you running away from me?" "I suppose I was."
There was brief scene cut out between Saavik and David on the bridge, paving the way for a later romance.
The original ending lacked Spock's tube on the Genesis planet, making it seem as if he really was dead. Meyer reshot it after studio pressure and a bad test screening.
(note)Although the new ending was intended to leave an opening for a sequel showing Spock's returning, many materials at the time seemed to show the public thought he was really dead, in particular the original DC comic book series.

TSFS:
A scene of Kirk and McCoy in the turbolift, where McCoy begins to show signs of acting like Spock.This appears in the DC comics adaptation, and checking the movie, the shot of Kirk in the turbolift cuts off right before this scene would occur.
The original sequence of events was intended to be Grissom approaching Genesis, and then Kirk and the Enterprise, and so on. This explains why the shot of the Grissom has the stardate over it. It is possible the film was scored before this change was made, as there is an abrupt shift in tone when the Enterprise appears after the credits.
The scene of McCoy in the bar originally had a longer ending, showing another guard attempting to apprehend him and McCoy trying to escape.
As Spock's body is being carried up to Mount Selaya, a young child whispers "Live Long and Prosper" to him

ST III was actually rejiggered very late in the editing process - check out either of the adaptations (comic or novelization) and it's clear the film was meant to lead off with Grissom arriving at the Genesis planet, then cut to the Enterprise, back to Genesis, then back to the Enterprise. That's why the special effect shot of Grissom has the stardate subtitle -- it was supposed to appear immediately after the opening titles.

I wonder if test audiences were asking who those people were on the Grissom, leading the studio/producers to decide to lead off with Kirk's log entry. I've always wanted to see that version, to see how it would play.

Carol/David extended intro conversation
Kirk reprising the 'blind as a tiberian bat' line as the orbit Regula
McCoy recognizing Terrell and mentioning they had served together
In the acedemy corridor as Kirk walks toward the lift, Spock says, "Something oppresses you."
Carol's Genesis naration was also re-recorded to imply more 'life-giving' properties--to give the audience more implication that Spock might have a chance at return
When Saavik says Reliant is near, Kirk says, "Isn't Chekov on Reliant?"

And the workprint contained virtually everything that CaptainBearclaw mentioned.

ST III was actually rejiggered very late in the editing process - check out either of the adaptations (comic or novelization) and it's clear the film was meant to lead off with Grissom arriving at the Genesis planet, then cut to the Enterprise, back to Genesis, then back to the Enterprise. That's why the special effect shot of Grissom has the stardate subtitle -- it was supposed to appear immediately after the opening titles.

I wonder if test audiences were asking who those people were on the Grissom, leading the studio/producers to decide to lead off with Kirk's log entry. I've always wanted to see that version, to see how it would play.

Click to expand...

The Laserdisc format could be easily copied to VHS--so years ago I re-edited the movie to match the script order--it was interesting, but David/Esteban and Nu-Saavik were clearly not up to carrying the majority of the first third of the movie.

-Scenes of Winona Kirk in the USS Kelvin sickbay were filmed, you can see a shot being prepared in the extras. They appear the early IMSDB script and novelization.

-Footage of Nero's wife Mandana was shot, of her stood in a green field. According to the early script, it was to be shown while Nero was tortured by the Klingons, showing us what he was seeing, that he was holding on and fighting to save her. She appears only briefly in he final movie, in a small and blurry hologram.

-I'm sure there was more to Nero's capture and time on Rura Penthe than has been released. Costumes for a Salt Vampire and a Gorn were made for those scenes.

-I'm curious how much from the early IMSDB script was actually filmed. Originally Spock intentionally went back in time by opening a second black hole, in order to save Romulus.

Star Trek Into Darkness...

-The B-roll shows several alternate and deleted scenes, including Kirk and Carol speaking in engineering.

-I'm curious where "The Shower of Evil" scene would have fitted into the movie. Before the explosion in London? After coming to the Enterprise from Kronos?

The famous prologue. Only thing to note here is that the score seems to just be an assembly of different Rosenman pieces.
A scene at Starfleet HQ showing Janice Rand once again.
Chapel meets Sarek outside the council chamber and tells him he's not too late.
Sarek is briefly interviewed by the Federation press.
Saavik and Kirk discussing her pregnancy.
A scene where Chekov's surgeon asks why Chekov hasn't been prepped for the surgery.
The famous scene of Sulu and his young great-grandfather. Never actually filmed due to child's stage fright.

TFF:
Some more scenes of Sybok's group making their way across the desert.
A scene of Sulu and Chekov passing Mount Rushmore, with an extra president.
Extra dialogue between the three ambassadors.
An additional scene of Spock's pain, showig him wishing to join Sybok's quest.
Rockman. A suprisingly decent effect. Unknown how much of him was shot.
A brief scene of Spock and McCoy talking in the officer's lounge.